{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualizing Multipore Zeolite Framework Classifications"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
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       "\n",
       "  if (window._bokeh_is_loading === 0) {\n",
       "    console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
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       "    load_libs(js_urls, function() {\n",
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       "  }\n",
       "}(this));"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import math\n",
    "import pandas as pd\n",
    "pd.options.display.max_rows = 240\n",
    "\n",
    "from bokeh.io import output_notebook\n",
    "from bokeh.plotting import figure, show, output_file\n",
    "from bokeh.charts import Bar\n",
    "from bokeh.charts.attributes import cat\n",
    "from bokeh.models import HoverTool, ColumnDataSource, FixedTicker\n",
    "from bokeh.palettes import Category10, Set1, Spectral, Set3, Viridis\n",
    "\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from zefram.utils import get_framework_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df = get_framework_data()\n",
    "\n",
    "df.rename(columns={'lcd': 'Largest cavity dia.', 'pld': 'Pore limiting dia.',\n",
    "                   'maxdsi': 'Max dia. of inc. sphere'}, inplace=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# prepare the data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def number_of_relevant_rings(rings):\n",
    "    'get the number of rings 6 < R < 13, +1 if there are any extra large rings'\n",
    "\n",
    "    s = sorted(i for i in rings if (13 > i > 6))\n",
    "    xl = sorted(i for i in rings if i > 12)\n",
    "    lenxl = 0\n",
    "    if len(xl) >= 1:\n",
    "        lenxl = 1\n",
    "    return len(s) + lenxl\n",
    "\n",
    "def ring_colors(rings):\n",
    "    'assign colors to specific ring sizes'\n",
    "\n",
    "    colors = {7 + i: Viridis[6][i] for i in range(6)}   \n",
    "    s = sorted(i for i in rings if (13 > i > 6))\n",
    "    out = [colors[r] for r in s]\n",
    "    \n",
    "    # add a grey color if there is an extra large ring\n",
    "    if any(r > 12 for r in rings):\n",
    "        out.append('#696969')\n",
    "    \n",
    "    if len(out) > 0:\n",
    "        return out\n",
    "\n",
    "df.loc[:, 'no_rings'] = df.rings.apply(number_of_relevant_rings)\n",
    "df.loc[:, 'ring_colors'] = df.rings.apply(ring_colors)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot with circle fractions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from sklearn.utils.extmath import cartesian\n",
    "    \n",
    "def show_plot_arcs(dataframe, width=750, height=300,radius=0.4, alpha=0.6, title=None, showit=True):\n",
    "\n",
    "    df = dataframe.copy()\n",
    "    \n",
    "    ncols = 15\n",
    "    nitems = df.shape[0]\n",
    "\n",
    "    if nitems % ncols == 0:\n",
    "        nrows = nitems / ncols\n",
    "    else:\n",
    "        nrows = nitems // ncols + 1\n",
    "\n",
    "    xy = cartesian([np.arange(nrows), np.arange(ncols)])\n",
    "\n",
    "    df.loc[:, 'x'] = xy[:nitems, 1]\n",
    "    df.loc[:, 'y'] = xy[:nitems, 0]\n",
    "\n",
    "    p = figure(title=title,\n",
    "                x_range = (df.x.min() - 0.5, df.x.max() + 0.5),\n",
    "                y_range = (df.y.max() + 0.5, df.y.min() - 0.5),\n",
    "                plot_width=width, plot_height=height, tools='save',\n",
    "                toolbar_location=\"above\")\n",
    "\n",
    "    \n",
    "    dmask = df['channel_dim'] > 1\n",
    "    # empty circles\n",
    "    x = df.loc[~dmask, 'x'].values\n",
    "    y = df.loc[~dmask, 'y'].values\n",
    "    p.circle(x, y, radius=radius, color='#ffffff', fill_alpha=1.0, line_color='#888888')\n",
    "    \n",
    "    # full circles\n",
    "    mask1 = dmask & (df['no_rings'] == 1)\n",
    "    x = df.loc[mask1, 'x'].values\n",
    "    y = df.loc[mask1, 'y'].values\n",
    "    \n",
    "    c = list(list(zip(*df.loc[mask1, 'ring_colors'].values.tolist()))[0])\n",
    "    p.circle(x, y, radius=radius, color=c, fill_alpha=alpha, line_color='#888888')\n",
    "    \n",
    "    # half circles/wedges\n",
    "    mask2 = dmask & (df['no_rings'] == 2)\n",
    "    x = df.loc[mask2, 'x'].values\n",
    "    y = df.loc[mask2, 'y'].values\n",
    "    c1, c2 = list(zip(*df.loc[mask2, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/4, end_angle=5*math.pi/4,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=5*math.pi/4, end_angle=math.pi/4,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # third circles/wedges\n",
    "    mask3 = dmask & (df['no_rings'] == 3)\n",
    "    x = df.loc[mask3, 'x'].values\n",
    "    y = df.loc[mask3, 'y'].values\n",
    "    c1, c2, c3 = list(zip(*df.loc[mask3, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/2, end_angle=7*math.pi/6,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=7*math.pi/6, end_angle=11*math.pi/6,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=11*math.pi/6, end_angle=math.pi/2,\n",
    "            color=list(c3), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # outer line\n",
    "    outer_colors = {'2d': Set1[5][4], '3d': Set1[5][0]}\n",
    "\n",
    "    d2mask = df['channel_dim'] == 2\n",
    "    x = df.loc[d2mask, 'x'].values\n",
    "    y = df.loc[d2mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.02, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['2d'], line_width=5.0, line_alpha=alpha)\n",
    "\n",
    "    d3mask = df['channel_dim'] == 3\n",
    "    x = df.loc[d3mask, 'x'].values\n",
    "    y = df.loc[d3mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.02, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['3d'], line_width=5.0, line_alpha=alpha)\n",
    "    \n",
    "    # legend\n",
    "    maxx = df['x'].max()\n",
    "    maxy = df['y'].max()\n",
    "    p.circle([x + 5.5 for x in range(7)], [maxy] * 7,\n",
    "             color=Viridis[6] + ['#696969'], radius=0.1, alpha=alpha)\n",
    "    p.circle([12.5, 13.5], [maxy] * 2,\n",
    "             color='#ffffff', radius=0.15, line_color=[outer_colors['2d'], outer_colors['3d']],\n",
    "             line_width=5.0, line_alpha=alpha)\n",
    "    p.text([x + 5.7 for x in range(9)], [maxy] * 9,\n",
    "           text=['7', '8', '9', '10', '11', '12', 'XL', '2D', '3D'],\n",
    "           text_alpha=0.7, text_align='left', text_baseline='middle')\n",
    "\n",
    "    text_props = {\n",
    "            \"text_font\": \"times\",\n",
    "            \"text_font_style\": \"bold\",\n",
    "            \"text_font_size\": \"13pt\",\n",
    "            \"angle\": 0,\n",
    "            \"color\": \"black\",\n",
    "            \"text_alpha\": 0.7,\n",
    "            \"text_align\": \"center\",\n",
    "            \"text_baseline\": \"middle\"\n",
    "        }\n",
    "\n",
    "    p.text(x=df.x.values, y=df.y.values, text=df.code.values, **text_props)\n",
    "    \n",
    "    p.grid.grid_line_color = None\n",
    "\n",
    "    p.axis[0].ticker.num_minor_ticks = 0\n",
    "    p.axis[1].ticker.num_minor_ticks = 0\n",
    "    p.axis.major_label_text_font_size = '0pt'\n",
    "    p.axis.major_tick_line_color = None\n",
    "\n",
    "    p.border_fill_color = 'white'\n",
    "    p.outline_line_width = 0\n",
    "    p.axis.visible = False\n",
    "\n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
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     "metadata": {},
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   ],
   "source": [
    "show_plot_arcs(df, width=900, height=900, radius=0.38, alpha=0.7)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Multipore zeolites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from sklearn.utils.extmath import cartesian\n",
    "    \n",
    "def has_multipores(rings):\n",
    "\n",
    "    s = sorted(i for i in rings if (13 > i > 6))\n",
    "    xl = sorted(i for i in rings if i > 12)\n",
    "\n",
    "    if len(s) + len(xl) >= 2:\n",
    "        return True\n",
    "    else:\n",
    "        return False\n",
    "    \n",
    "def show_plot_arcs_multipore(dataframe, width=750, height=300, radius=0.4, alpha=0.6, title=None, showit=True):\n",
    "\n",
    "    df = dataframe.copy()\n",
    "    \n",
    "    ncols = 15\n",
    "    nitems = df.shape[0]\n",
    "\n",
    "    if nitems % ncols == 0:\n",
    "        nrows = nitems / ncols\n",
    "    else:\n",
    "        nrows = nitems // ncols + 1\n",
    "\n",
    "    xy = cartesian([np.arange(nrows), np.arange(ncols)])\n",
    "\n",
    "    df.loc[:, 'x'] = xy[:nitems, 1]\n",
    "    df.loc[:, 'y'] = xy[:nitems, 0]\n",
    "\n",
    "    p = figure(title=title,\n",
    "                x_range = (df.x.min() - 0.5, df.x.max() + 0.5),\n",
    "                y_range = (df.y.max() + 0.5, df.y.min() - 0.5),\n",
    "                plot_width=width, plot_height=height, tools='save',\n",
    "                toolbar_location=\"above\")\n",
    "\n",
    "    \n",
    "    mmask = (df['channel_dim'] > 1) & df.rings.apply(has_multipores)\n",
    "    # empty circles\n",
    "    x = df.loc[~mmask, 'x'].values\n",
    "    y = df.loc[~mmask, 'y'].values\n",
    "    p.circle(x, y, radius=radius, color='#ffffff', fill_alpha=1.0, line_color='#888888')\n",
    "\n",
    "    # full circles special case or the IRY framework\n",
    "    mask1 = (df['no_rings'] == 1) & mmask\n",
    "    x = df.loc[mask1, 'x'].values\n",
    "    y = df.loc[mask1, 'y'].values\n",
    "    c = list(list(zip(*df.loc[mask1, 'ring_colors'].values.tolist()))[0])\n",
    "    p.circle(x, y, radius=radius, color=c, fill_alpha=alpha, line_color='#888888')\n",
    "    \n",
    "    # half circles/wedges\n",
    "    mask2 = mmask & (df['no_rings'] == 2)\n",
    "    x = df.loc[mask2, 'x'].values\n",
    "    y = df.loc[mask2, 'y'].values\n",
    "    c1, c2 = list(zip(*df.loc[mask2, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/4, end_angle=5*math.pi/4,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=5*math.pi/4, end_angle=math.pi/4,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # third circles/wedges\n",
    "    mask3 = mmask & (df['no_rings'] == 3)\n",
    "    x = df.loc[mask3, 'x'].values\n",
    "    y = df.loc[mask3, 'y'].values\n",
    "    c1, c2, c3 = list(zip(*df.loc[mask3, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/2, end_angle=7*math.pi/6,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=7*math.pi/6, end_angle=11*math.pi/6,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=11*math.pi/6, end_angle=math.pi/2,\n",
    "            color=list(c3), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # outer line\n",
    "    outer_colors = {'2d': Set1[5][4], '3d': Set1[5][0]}\n",
    "\n",
    "    d2mask = (df['channel_dim'] == 2) & mmask\n",
    "    x = df.loc[d2mask, 'x'].values\n",
    "    y = df.loc[d2mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.02, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['2d'], line_width=5.0, line_alpha=alpha)\n",
    "\n",
    "    d3mask = (df['channel_dim'] == 3) & mmask\n",
    "    x = df.loc[d3mask, 'x'].values\n",
    "    y = df.loc[d3mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.02, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['3d'], line_width=5.0, line_alpha=alpha)\n",
    "    \n",
    "    # legend\n",
    "    maxx = df['x'].max()\n",
    "    maxy = df['y'].max()\n",
    "    p.circle([x + 5.5 for x in range(7)], [maxy] * 7,\n",
    "             color=Viridis[6] + ['#696969'], radius=0.1, alpha=alpha)\n",
    "    p.circle([12.5, 13.5], [maxy] * 2,\n",
    "             color='#ffffff', radius=0.15, line_color=[outer_colors['2d'], outer_colors['3d']],\n",
    "             line_width=5.0, line_alpha=alpha)\n",
    "    p.text([x + 5.7 for x in range(9)], [maxy] * 9,\n",
    "           text=['7', '8', '9', '10', '11', '12', 'XL', '2D', '3D'],\n",
    "           text_alpha=0.7, text_align='left', text_baseline='middle')\n",
    "\n",
    "    text_props = {\n",
    "            \"text_font\": \"times\",\n",
    "            \"text_font_style\": \"bold\",\n",
    "            \"text_font_size\": \"13pt\",\n",
    "            \"angle\": 0,\n",
    "            \"color\": \"black\",\n",
    "            \"text_alpha\": 0.7,\n",
    "            \"text_align\": \"center\",\n",
    "            \"text_baseline\": \"middle\"\n",
    "        }\n",
    "\n",
    "    p.text(x=df.x.values, y=df.y.values, text=df.code.values, **text_props)\n",
    "    \n",
    "    p.grid.grid_line_color = None\n",
    "\n",
    "    p.axis[0].ticker.num_minor_ticks = 0\n",
    "    p.axis[1].ticker.num_minor_ticks = 0\n",
    "    p.axis.major_label_text_font_size = '0pt'\n",
    "    p.axis.major_tick_line_color = None\n",
    "\n",
    "    p.border_fill_color = 'white'\n",
    "    p.outline_line_width = 0\n",
    "    p.axis.visible = False\n",
    "\n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
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   "source": [
    "show_plot_arcs_multipore(df, width=900, height=900, radius=0.38, alpha=0.7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {
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   "source": [
    "def show_plot_arcs_multipore_only(dataframe, width=750, height=300, radius=0.4, alpha=0.6, title=None, showit=True):\n",
    "\n",
    "    df = dataframe.copy()\n",
    "    \n",
    "    ncols = 9\n",
    "    nitems = df.shape[0]\n",
    "\n",
    "    if nitems % ncols == 0:\n",
    "        nrows = nitems / ncols\n",
    "    else:\n",
    "        nrows = nitems // ncols + 1\n",
    "\n",
    "    xy = cartesian([np.arange(nrows), np.arange(ncols)])\n",
    "\n",
    "    df.loc[:, 'x'] = xy[:nitems, 1]\n",
    "    df.loc[:, 'y'] = xy[:nitems, 0]\n",
    "\n",
    "    p = figure(title=title,\n",
    "                x_range = (df.x.min() - 0.5, df.x.max() + 0.5),\n",
    "                y_range = (df.y.max() + 1.5, df.y.min() - 0.5),\n",
    "                plot_width=width, plot_height=height, tools='save',\n",
    "                toolbar_location=\"above\")\n",
    "\n",
    "    # full circles special case or the IRY framework\n",
    "    mask1 = (df['no_rings'] == 1)\n",
    "    x = df.loc[mask1, 'x'].values\n",
    "    y = df.loc[mask1, 'y'].values\n",
    "    c = list(list(zip(*df.loc[mask1, 'ring_colors'].values.tolist()))[0])\n",
    "    p.circle(x, y, radius=radius, color=c, fill_alpha=alpha, line_color='#888888')\n",
    "    \n",
    "    # half circles/wedges\n",
    "    mask2 = (df['no_rings'] == 2)\n",
    "    x = df.loc[mask2, 'x'].values\n",
    "    y = df.loc[mask2, 'y'].values\n",
    "    c1, c2 = list(zip(*df.loc[mask2, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/4, end_angle=5*math.pi/4,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=5*math.pi/4, end_angle=math.pi/4,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # third circles/wedges\n",
    "    mask3 = (df['no_rings'] == 3)\n",
    "    x = df.loc[mask3, 'x'].values\n",
    "    y = df.loc[mask3, 'y'].values\n",
    "    c1, c2, c3 = list(zip(*df.loc[mask3, 'ring_colors'].values.tolist()))\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/2, end_angle=7*math.pi/6,\n",
    "            color=list(c1), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=7*math.pi/6, end_angle=11*math.pi/6,\n",
    "            color=list(c2), alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=11*math.pi/6, end_angle=math.pi/2,\n",
    "            color=list(c3), alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # outer line\n",
    "    outer_colors = {'2d': Set1[5][4], '3d': Set1[5][0]}\n",
    "\n",
    "    #m23mask = (df['no_rings'] == 2) | (df['no_rings'] == 3)\n",
    "    d2mask = (df['channel_dim'] == 2)# & m23mask\n",
    "    x = df.loc[d2mask, 'x'].values\n",
    "    y = df.loc[d2mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.03, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['2d'], line_width=7.0, line_alpha=alpha)\n",
    "\n",
    "    d3mask = (df['channel_dim'] == 3)# & m23mask\n",
    "    x = df.loc[d3mask, 'x'].values\n",
    "    y = df.loc[d3mask, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.03, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=outer_colors['3d'], line_width=7.0, line_alpha=alpha)\n",
    "    \n",
    "    # legend\n",
    "    maxx = df['x'].max()\n",
    "    maxy = df['y'].max()\n",
    "    p.circle([x  for x in range(7)], [maxy + 1] * 7,\n",
    "             color=Viridis[6] + ['#696969'], radius=0.1, alpha=alpha)\n",
    "    p.circle([7.0, 8.0], [maxy + 1] * 2,\n",
    "             color='#ffffff', radius=0.15, line_color=[outer_colors['2d'], outer_colors['3d']],\n",
    "             line_width=5.0, line_alpha=alpha)\n",
    "    p.text([x + 0.2 for x in range(9)], [maxy + 1] * 9,\n",
    "           text=['7', '8', '9', '10', '11', '12', 'XL', '2D', '3D'],\n",
    "           text_alpha=0.7, text_align='left', text_baseline='middle')\n",
    "\n",
    "    text_props = {\n",
    "            \"text_font\": \"times\",\n",
    "            \"text_font_style\": \"bold\",\n",
    "            \"text_font_size\": \"13pt\",\n",
    "            \"angle\": 0,\n",
    "            \"color\": \"black\",\n",
    "            \"text_alpha\": 0.7,\n",
    "            \"text_align\": \"center\",\n",
    "            \"text_baseline\": \"middle\"\n",
    "        }\n",
    "\n",
    "    p.text(x=df.x.values, y=df.y.values, text=df.code.values, **text_props)\n",
    "    \n",
    "    p.grid.grid_line_color = None\n",
    "\n",
    "    p.axis[0].ticker.num_minor_ticks = 0\n",
    "    p.axis[1].ticker.num_minor_ticks = 0\n",
    "    p.axis.major_label_text_font_size = '0pt'\n",
    "    p.axis.major_tick_line_color = None\n",
    "\n",
    "    p.border_fill_color = 'white'\n",
    "    p.outline_line_width = 0\n",
    "    p.axis.visible = False\n",
    "\n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
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   "source": [
    "mask = (df['channel_dim'] > 1) & df.rings.apply(has_multipores)\n",
    "show_plot_arcs_multipore_only(df[mask], width=900, height=900, radius=0.38, alpha=0.7)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bar charts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def multid_bar_plot(data, sizes, title=None, showit=True, dropna=True):\n",
    "    '''\n",
    "    plot a bar chart for a given category\n",
    "    \n",
    "    Args:\n",
    "        data (pd.DataFrame) :\n",
    "        \n",
    "        sizes: list of ring sizes e.g. [8, 10], [8, 10, 12]\n",
    "\n",
    "    '''\n",
    "\n",
    "    def in_list(rings, sizes):\n",
    "        'obtain the mask'\n",
    "\n",
    "        if set(sizes).issubset(set(rings)) and max(rings) == max(sizes):\n",
    "            return True\n",
    "        else:\n",
    "            return False\n",
    "    \n",
    "    ring_mask = df.rings.apply(in_list, sizes=sizes)\n",
    "    mask = (df['channel_dim'] > 1) & ring_mask\n",
    "    cols = ['code', 'Largest cavity dia.', 'Pore limiting dia.', 'Max dia. of inc. sphere']\n",
    "    melted = pd.melt(data.loc[mask, cols].dropna().sort_values(by='Largest cavity dia.'),\n",
    "                     id_vars=['code'], value_vars=cols[1:])\n",
    "\n",
    "    p = Bar(melted, label=cat('code', sort=False), values=\"value\", group=\"variable\",\n",
    "            legend=\"top_left\", xlabel='Framework code', ylabel='Length [Angstrom]',\n",
    "            plot_width=900, title=title, toolbar_location=\"above\")\n",
    "    \n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
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       "       \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "       \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "       \"</p>\\n\"+\n",
       "       \"<ul>\\n\"+\n",
       "       \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "       \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
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       "       \"<code>\\n\"+\n",
       "       \"from bokeh.resources import INLINE\\n\"+\n",
       "       \"output_notebook(resources=INLINE)\\n\"+\n",
       "       \"</code>\\n\"+\n",
       "       \"</div>\"}};\n",
       "  \n",
       "    function display_loaded() {\n",
       "      if (window.Bokeh !== undefined) {\n",
       "        var el = document.getElementById(\"152ede7b-3b24-4461-a490-b1480f8681e5\");\n",
       "        el.textContent = \"BokehJS \" + Bokeh.version + \" successfully loaded.\";\n",
       "      } else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(display_loaded, 100)\n",
       "      }\n",
       "    }\n",
       "  \n",
       "    function run_callbacks() {\n",
       "      window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n",
       "      delete window._bokeh_onload_callbacks\n",
       "      console.info(\"Bokeh: all callbacks have finished\");\n",
       "    }\n",
       "  \n",
       "    function load_libs(js_urls, callback) {\n",
       "      window._bokeh_onload_callbacks.push(callback);\n",
       "      if (window._bokeh_is_loading > 0) {\n",
       "        console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "        return null;\n",
       "      }\n",
       "      if (js_urls == null || js_urls.length === 0) {\n",
       "        run_callbacks();\n",
       "        return null;\n",
       "      }\n",
       "      console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "      window._bokeh_is_loading = js_urls.length;\n",
       "      for (var i = 0; i < js_urls.length; i++) {\n",
       "        var url = js_urls[i];\n",
       "        var s = document.createElement('script');\n",
       "        s.src = url;\n",
       "        s.async = false;\n",
       "        s.onreadystatechange = s.onload = function() {\n",
       "          window._bokeh_is_loading--;\n",
       "          if (window._bokeh_is_loading === 0) {\n",
       "            console.log(\"Bokeh: all BokehJS libraries loaded\");\n",
       "            run_callbacks()\n",
       "          }\n",
       "        };\n",
       "        s.onerror = function() {\n",
       "          console.warn(\"failed to load library \" + url);\n",
       "        };\n",
       "        console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "      }\n",
       "    };var element = document.getElementById(\"152ede7b-3b24-4461-a490-b1480f8681e5\");\n",
       "    if (element == null) {\n",
       "      console.log(\"Bokeh: ERROR: autoload.js configured with elementid '152ede7b-3b24-4461-a490-b1480f8681e5' but no matching script tag was found. \")\n",
       "      return false;\n",
       "    }\n",
       "  \n",
       "    var js_urls = [];\n",
       "  \n",
       "    var inline_js = [\n",
       "      function(Bokeh) {\n",
       "        (function() {\n",
       "          var fn = function() {\n",
       "            var docs_json = 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   "source": [
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       "            console.log(\"Bokeh: all BokehJS libraries loaded\");\n",
       "            run_callbacks()\n",
       "          }\n",
       "        };\n",
       "        s.onerror = function() {\n",
       "          console.warn(\"failed to load library \" + url);\n",
       "        };\n",
       "        console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "      }\n",
       "    };var element = document.getElementById(\"62bbb953-ad04-4586-946e-e4f2e6b32bdf\");\n",
       "    if (element == null) {\n",
       "      console.log(\"Bokeh: ERROR: autoload.js configured with elementid '62bbb953-ad04-4586-946e-e4f2e6b32bdf' but no matching script tag was found. \")\n",
       "      return false;\n",
       "    }\n",
       "  \n",
       "    var js_urls = [];\n",
       "  \n",
       "    var inline_js = [\n",
       "      function(Bokeh) {\n",
       "        (function() {\n",
       "          var fn = function() {\n",
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   "source": [
    "multid_bar_plot(df, [8, 12], title='Multipore frameworks with 8 and 12 MR')"
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     "metadata": {},
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   ],
   "source": [
    "multid_bar_plot(df, [10, 12], title='Multipore frameworks with 10 and 12 MR')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
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       "            \n",
       "            Bokeh.embed.embed_items(docs_json, render_items);\n",
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       "          if (document.readyState != \"loading\") fn();\n",
       "          else document.addEventListener(\"DOMContentLoaded\", fn);\n",
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       "      },\n",
       "      function(Bokeh) {\n",
       "      }\n",
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       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "        window._bokeh_failed_load = true;\n",
       "      } else if (force !== true) {\n",
       "        var cell = $(document.getElementById(\"74920339-2a6b-484a-a900-2f146b5294ea\")).parents('.cell').data().cell;\n",
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       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
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       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
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       "</script>"
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   ],
   "source": [
    "multid_bar_plot(df, [8, 10, 12], title='Multipore frameworks with 8, 10, 12 MR')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
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       "<table><tr><th>Software</th><th>Version</th></tr><tr><td>Python</td><td>3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]</td></tr><tr><td>IPython</td><td>6.0.0</td></tr><tr><td>OS</td><td>Linux 3.16.0 4 amd64 x86_64 with debian 8.8</td></tr><tr><td>bokeh</td><td>0.12.5</td></tr><tr><td>pandas</td><td>0.20.1</td></tr><tr><td>numpy</td><td>1.12.1</td></tr><tr><td>zefram</td><td>0.1.2</td></tr><tr><td colspan='2'>Tue May 23 22:29:32 2017 CEST</td></tr></table>"
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       "\\begin{tabular}{|l|l|}\\hline\n",
       "{\\bf Software} & {\\bf Version} \\\\ \\hline\\hline\n",
       "Python & 3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] \\\\ \\hline\n",
       "IPython & 6.0.0 \\\\ \\hline\n",
       "OS & Linux 3.16.0 4 amd64 x86\\_64 with debian 8.8 \\\\ \\hline\n",
       "bokeh & 0.12.5 \\\\ \\hline\n",
       "pandas & 0.20.1 \\\\ \\hline\n",
       "numpy & 1.12.1 \\\\ \\hline\n",
       "zefram & 0.1.2 \\\\ \\hline\n",
       "\\hline \\multicolumn{2}{|l|}{Tue May 23 22:29:32 2017 CEST} \\\\ \\hline\n",
       "\\end{tabular}\n"
      ],
      "text/plain": [
       "Software versions\n",
       "Python 3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]\n",
       "IPython 6.0.0\n",
       "OS Linux 3.16.0 4 amd64 x86_64 with debian 8.8\n",
       "bokeh 0.12.5\n",
       "pandas 0.20.1\n",
       "numpy 1.12.1\n",
       "zefram 0.1.2\n",
       "Tue May 23 22:29:32 2017 CEST"
      ]
     },
     "execution_count": 62,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%version_information bokeh, pandas, numpy, zefram"
   ]
  }
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